diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index b36920ca4947bec7706017c357c50aa419b1dca0..a0275cca6d3c6da59a025d8e769519292a5f03b7 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -100,7 +100,7 @@ def generate_sa(fastq, reference):
     with open(sai, 'w') as sai_file:
         bwa_command = "bwa aln %s -t %d %s %s" \
                 % (bwa_aln_params, cpu_count(),
-                   reference, fastq, sai_file)
+                   reference, fastq)
 
         logger.info("Running bwa with %s", bwa_command)
         subprocess.check_call(shlex.split(bwa_command), stdout=sai_file)